Hybridizing Non-dominated Sorting Algorithms: Divide-and-Conquer Meets Best Order Sort

Many production-grade algorithms benefit from combining an asymptotically efficient algorithm for solving big problem instances, by splitting them into smaller ones, and an asymptotically inefficient algorithm with a very small implementation constant for solving small subproblems. A well-known example is stable sorting, where mergesort is often combined with insertion sort to achieve a constant but noticeable speed-up. We apply this idea to non-dominated sorting. Namely, we combine the divide-and-conquer algorithm, which has the currently best known asymptotic runtime of $O(N (\log N)^{M - 1})$, with the Best Order Sort algorithm, which has the runtime of $O(N^2 M)$ but demonstrates the best practical performance out of quadratic algorithms. Empirical evaluation shows that the hybrid's running time is typically not worse than of both original algorithms, while for large numbers of points it outperforms them by at least 20%. For smaller numbers of objectives, the speedup can be as large as four times.Comment: A two-page abstract of this paper will appear in the proceedings companion of the 2017 Genetic and Evolutionary Computation Conference (GECCO 2017

Combinatorial and Asymptotical Results on the Neighborhood Grid

In 2009, Joselli et al introduced the Neighborhood Grid data structure for fast computation of neighborhood estimates in point clouds. Even though the data structure has been used in several applications and shown to be practically relevant, it is theoretically not yet well understood. The purpose of this paper is to present a polynomial-time algorithm to build the data structure. Furthermore, it is investigated whether the presented algorithm is optimal. This investigations leads to several combinatorial questions for which partial results are given. Finally, we present several limits and experiments regarding the quality of the obtained neighborhood relation.Comment: 33 pages, 18 Figure

GPU-Accelerated BWT Construction for Large Collection of Short Reads

Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many state-of-the-art aligners, at their core, have used the Burrows-Wheeler transform (BWT) as a main-memory index of a reference genome (typical example, NCBI human genome). Recently, BWT has also found its use in string-graph assembly, for indexing the reads (i.e., raw data from DNA sequencers). In a typical data set, the volume of reads is tens of times of the sequenced genome and can be up to 100 Gigabases. Note that a reference genome is relatively stable and computing the index is not a frequent task. For reads, the index has to computed from scratch for each given input. The ability of efficient BWT construction becomes a much bigger concern than before. In this paper, we present a practical method called CX1 for constructing the BWT of very large string collections. CX1 is the first tool that can take advantage of the parallelism given by a graphics processing unit (GPU, a relative cheap device providing a thousand or more primitive cores), as well as simultaneously the parallelism from a multi-core CPU and more interestingly, from a cluster of GPU-enabled nodes. Using CX1, the BWT of a short-read collection of up to 100 Gigabases can be constructed in less than 2 hours using a machine equipped with a quad-core CPU and a GPU, or in about 43 minutes using a cluster with 4 such machines (the speedup is almost linear after excluding the first 16 minutes for loading the reads from the hard disk). The previously fastest tool BRC is measured to take 12 hours to process 100 Gigabases on one machine; it is non-trivial how BRC can be parallelized to take advantage a cluster of machines, let alone GPUs.Comment: 11 page

Fast construction of FM-index for long sequence reads

Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse (complement) lexicographical order without a separate sorting step. The implementation is among the fastest for indexing short reads and the only one that practically works for reads of averaged kilobases in length. Availability and implementation: https://github.com/lh3/ropebwt2 Contact: [email protected]: 2 page